Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate Ga0059261_4003 Ga0059261_4003 aspartate-semialdehyde dehydrogenase (peptidoglycan organisms)
Query= SwissProt::P23247 (337 letters) >FitnessBrowser__Korea:Ga0059261_4003 Length = 341 Score = 326 bits (836), Expect = 5e-94 Identities = 178/335 (53%), Positives = 225/335 (67%), Gaps = 7/335 (2%) Query: 5 FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFN--GKTVRVQNVEEF 62 + V + GATG VG ML +L EREFP+DEL +LAS RS G F GK ++QN+E F Sbjct: 3 YRVVVAGATGNVGREMLNILAEREFPIDELAVLASSRSTGDMVDFGETGKQYKIQNIEHF 62 Query: 63 DWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFR 122 D + +ALF+ G E + AP A AG VIDN+S +R D D+PL+VPEVNPEAI ++ Sbjct: 63 DPTGWDMALFAIGSEATKVHAPRFAAAGCTVIDNSSLYRMDPDVPLIVPEVNPEAIDGYK 122 Query: 123 NRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNG 182 +NIIANPNCST QM+VALKP++DA G++R+ V TYQSVSGAGK G+DEL Q+ + G Sbjct: 123 AKNIIANPNCSTAQMVVALKPLHDAAGVKRVVVATYQSVSGAGKEGMDELFEQSRNIFVG 182 Query: 183 YPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVF 242 AE F++QIAFN IP ID F+D+GYTKEE KMV ET+KI DP + V TCVRVPVF Sbjct: 183 DQAEPKKFTKQIAFNVIPHIDSFLDDGYTKEEWKMVVETKKIL-DPKVKVTATCVRVPVF 241 Query: 243 YGHAEAVHVETRAPIDAEQVMDMLEQTDGIELF---RGADFPTQVRDAGGKDHVLVGRVR 299 GH+EAV+VE + AE +L + GI L + T V + G V RVR Sbjct: 242 VGHSEAVNVELERELSAEDAQKILREAPGIMLVDKREDGGYVTPV-ECVGDYATFVSRVR 300 Query: 300 NDISHHSGINLWVVADNVRKGAATNAVQIAELLVR 334 D++ +G+ W V+DN+RKGAA NAVQIAELL R Sbjct: 301 EDVTVENGLAFWCVSDNLRKGAALNAVQIAELLGR 335 Lambda K H 0.319 0.135 0.395 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 335 Number of extensions: 15 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 337 Length of database: 341 Length adjustment: 28 Effective length of query: 309 Effective length of database: 313 Effective search space: 96717 Effective search space used: 96717 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
Align candidate Ga0059261_4003 Ga0059261_4003 (aspartate-semialdehyde dehydrogenase (peptidoglycan organisms))
to HMM TIGR01296 (asd: aspartate-semialdehyde dehydrogenase (EC 1.2.1.11))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR01296.hmm # target sequence database: /tmp/gapView.20571.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01296 [M=339] Accession: TIGR01296 Description: asd_B: aspartate-semialdehyde dehydrogenase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-142 458.8 0.1 6.2e-142 458.6 0.1 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_4003 Ga0059261_4003 aspartate-semiald Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_4003 Ga0059261_4003 aspartate-semialdehyde dehydrogenase (peptidoglycan organism # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 458.6 0.1 6.2e-142 6.2e-142 2 336 .. 5 333 .. 4 336 .. 0.98 Alignments for each domain: == domain 1 score: 458.6 bits; conditional E-value: 6.2e-142 TIGR01296 2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfk..gkeleveeaekesfegidialfs 68 v + GatG+vG+e+l++L+er+fpid+l +las+rs+G v f gk+++++++e++++ g d+alf+ lcl|FitnessBrowser__Korea:Ga0059261_4003 5 VVVAGATGNVGREMLNILAEREFPIDELAVLASSRSTGDMVDFGetGKQYKIQNIEHFDPTGWDMALFA 73 7899***************************************63379********************* PP TIGR01296 69 aGgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLk 137 G+ k+ ap++a+ag++viDn+s++r+d+dvPL+vpevn e + k k+iianPnCst q+vv+Lk lcl|FitnessBrowser__Korea:Ga0059261_4003 74 IGSEATKVHAPRFAAAGCTVIDNSSLYRMDPDVPLIVPEVNPEAIDGYKAKNIIANPNCSTAQMVVALK 142 ********************************************************************* PP TIGR01296 138 plkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidk 206 pl+d+a++krvvv+tYq+vsGaGk+g++eL +q + +++g ep kkf+kqiafn+ip+id+ lcl|FitnessBrowser__Korea:Ga0059261_4003 143 PLHDAAGVKRVVVATYQSVSGAGKEGMDELFEQSRNIFVGDQAEP-------KKFTKQIAFNVIPHIDS 204 ****************************************99997.......9**************** PP TIGR01296 207 lkedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvv 275 + +dGytkee k++ et+kil+ +++kv+atcvrvPvf+ghse+v++e+e+els+e+++++L+eapg++ lcl|FitnessBrowser__Korea:Ga0059261_4003 205 FLDDGYTKEEWKMVVETKKILD-PKVKVTATCVRVPVFVGHSEAVNVELERELSAEDAQKILREAPGIM 272 **********************.********************************************** PP TIGR01296 276 viddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaell 336 ++d+ ++ y+tP+e vg ++fv+r+r+D++ e+gla ++v+DnlrkGaalnavqiaell lcl|FitnessBrowser__Korea:Ga0059261_4003 273 LVDKREDGGYVTPVECVGDYATFVSRVREDVTVENGLAFWCVSDNLRKGAALNAVQIAELL 333 ***********************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (341 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10.40 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory